rdock-list-def — General Mailing List for rDock users

[rDock-list-def] Rotable ligand bonds define

[Matteo U. <m....@ho...>]

Dear All.


Can you tell if is it possible to define which bonds are able to rotate (or not) in the ligand during the docking?

If I understand the program use a full flexible ligand, so does it allow the double bounds rotation?


For example, I'm trying to dock a ligand with an alkene chain and some bounds are in a resonance form. I don't want it to rotate.


Can you help me?


Matteo.

[rDock-list-def] How to add parameters to rDock force field?

[Jose M. G. <jos...@un...>]

Dear rDock community,

I would like to dock some sulfonamides, but noticed they all get a very 
high score.
By reading the $RBT_ROOT/data/sf/Tripos52_dihedrals.prm file, I saw that 
sulfonamides were actually currently not supported.
I would like to modify the force field to add them.

How would you recommand I do that?

As an extra question, I noticed that the intramolecular score does not 
take into account interatomic distances, so unlikely conformers can 
still get a good score.
Is it possible to consider them while assessing pose scores?

Thank you in advance for your replies and have a very nice day.

Cheers,
Jose Manuel

[rDock-list-def] Fixing the terminal OH and NH3+ of some residues

[Noelly M. <mad...@ho...>]

                                                                                                                                                                                                    
                                                                                                                Dear all, 

According to the manual, the parameter RECEPTOR_FLEX defines terminal OH and NH3+ groups within a given 
 distance of docking volume as flexible.

During the docking step, I would like to treat the terminal OH and NH3+ of some residues as flexible
(using the RECEPTOR_FLEX parameter), and some as fixed.
 
Is there a parameter that allow me to fix the terminal OH or NH3+ of specific residues even if
they are within the distance specified in the RECEPTOR_FLEX parameter?

If not, is there a way to fix some residues while others are flexible?


Thank you for your help,

Best regards,
Noelly.
 		 	   		  

[rDock-list-def] (no subject)

[Noelly M. <mad...@ho...>]

Dear all, 


According to the manual, the parameter RECEPTOR_FLEX defines terminal OH and NH3+ groups within a given 
 distance of docking volume as flexible.

During the docking step, I would like to treat the terminal OH and NH3+ of some residues as flexible
(using the RECEPTOR_FLEX parameter), and some as fixed.
 
Is there a parameter that allow me to fix the terminal OH or NH3+ of specific residues even if
they are within the chosen distance in the RECEPTOR_FLEX parameter?


Thank you for your help,

Best regards,
Noelly.


 		 	   		  

Re: [rDock-list-def] Error with the two sphere method

[Sergio R. C. <sru...@gm...>]

Dear Noelly,

I think the error is in the SITE_MAPPER parameter.
You should change the "RbtLigandSiteMapper", which corresponds to the
reference ligand method, to "RbtSphereSiteMapper" and re-run rbcavity.
The prm section should be something like this, depending on the rest of
your parameters:

################################################################
> # CAVITY DEFINITION: TWO SPHERES METHOD
> ################################################################
> SECTION MAPPER
>     SITE_MAPPER RbtSphereSiteMapper
>     CENTER (7.185,8.250,22.649)
>     RADIUS 15.0
>     SMALL_SPHERE 1.5
>     LARGE_SPHERE 6.0
>     MAX_CAVITIES 1
> END_SECTION


Best,

Sergio



2016-03-03 12:51 GMT+01:00 Noelly MADELEINE <mad...@ho...>:

> Dear All,
>
> I am actually learning to use rDOCK. And I have a problem with the
> generation of the docking site.
>
> Because I don't have any reference ligand, I would like to use the two
> sphere method to define the region (cavity definition).
> To prepare my system definition file, I took the example you gave in a
> tutorial. I replaced the parameter "REF_MOL" by "CENTER" and the parameter
> "LARGE_SPHERE" was added.
>
> Here you have my prm file:
>
> RBT_PARAMETER_FILE_V1.00
> TITLE TEST
>
> RECEPTOR_FILE test.mol2
> RECEPTOR_FLEX 3.0
>
> ##################################################################
> ### CAVITY DEFINITION: TWO SPHERE METHOD
> ##################################################################
> SECTION MAPPER
>     SITE_MAPPER RbtLigandSiteMapper
>     CENTER (11.2290,32.3770,28.9710)
>     RADIUS 10.0
>     SMALL_SPHERE 1.5
>     LARGE_SPHERE 4.0
>     MAX_CAVITIES 99
>     VOL_INCR 0.0
>     GRIDSTEP 0.5
>     MIN_VOLUME 100
> END_SECTION
>
> #################################
> #CAVITY RESTRAINT PENALTY
> #################################
> SECTION CAVITY
>     SCORING_FUNCTION RbtCavityGridSF
>     WEIGHT 1.0
> END_SECTION
>
>
> When I use the command line:  rbcavity -was -d -r test.prm
>
> this error appears:
>
> Command line arguments:
> -r cd80.prm
> -was
> -d
> RBT_BAD_ARGUMENT at ../src/lib/RbtParamHandler.cxx, line 66
> Undefined parameter CENTER
>
>
> Is there a mistake on the prm file?
>
> Thank you for your help.
>
> Best regards,
> Noelly
>
>
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[rDock-list-def] Error with the two sphere method

[Noelly M. <mad...@ho...>]

Dear All,

I am actually learning to use rDOCK. And I have a problem with the generation of the docking site.

Because I don't have any reference ligand, I would like to use the two sphere method to define the region (cavity definition).
To prepare my system definition file, I took the example you gave in a tutorial. I replaced the parameter "REF_MOL" by "CENTER" and the parameter "LARGE_SPHERE" was added.

Here you have my prm file:

RBT_PARAMETER_FILE_V1.00
TITLE TEST

RECEPTOR_FILE test.mol2
RECEPTOR_FLEX 3.0

##################################################################
### CAVITY DEFINITION: TWO SPHERE METHOD
##################################################################
SECTION MAPPER
    SITE_MAPPER RbtLigandSiteMapper
    CENTER (11.2290,32.3770,28.9710)
    RADIUS 10.0
    SMALL_SPHERE 1.5
    LARGE_SPHERE 4.0
    MAX_CAVITIES 99
    VOL_INCR 0.0
    GRIDSTEP 0.5
    MIN_VOLUME 100
END_SECTION

#################################
#CAVITY RESTRAINT PENALTY
#################################
SECTION CAVITY
    SCORING_FUNCTION RbtCavityGridSF
    WEIGHT 1.0
END_SECTION


When I use the command line:  rbcavity -was -d -r test.prm 

this error appears:

Command line arguments:
-r cd80.prm
-was
-d
RBT_BAD_ARGUMENT at ../src/lib/RbtParamHandler.cxx, line 66
Undefined parameter CENTER


Is there a mistake on the prm file?

Thank you for your help.

Best regards,
Noelly
 		 	   		  

Re: [rDock-list-def] extract score from rescoring without writing a sd file

[Sergio R. C. <sru...@gm...>]

Dear Jose Manuel,

Sorry for the delay.
I am afraid there is not any trivial solution to what you are asking.
rDock needs an output file to write the results on-the-fly.
A workaround that I would suggest you is to run "sdreport -t OUTPUTFILE.sd
> OUTPUTFILE_scores.txt" just after each job is finished to save all the
different scores and then remove "OUTPUTFILE.sd".
The function of the -t argument for rbdock is to control how many runs for
each ligand are performed and which of the docking poses generated are
written depending on the score, but it is not related to the creation or
not of the output file independently from the scoring.
Best,

Sergio


2015-12-18 17:26 GMT+01:00 Jose Manuel Gally <
jos...@un...>:

> Hi,
>
> I rescore poses using rbdock with the score.prm protocol as routine on a
> single molecule within a script.
>
> I would like to avoid writing output files and just extract the SCORE
> and SCORE.INTER properties directly from the STDOUT.
> However, when I remove the -o argument, I cannot access the scores at
> all and something like -o /dev/stdout returns an error since the
> programme still wants to write a file.
>
> Is there a way to achieve this without modifying the source code (I
> don't know much about C++...!)?
> If not, could you kindly tell me what I should change in the rbdock.cxx
> to make it work?
>
> I also tried to use the -T argument but could not find the scores among
> the displayed info. Did I miss something?
>
> Thank you for your help!
>
> Cheers,
> Jose Manuel
>
> Supplementary information:
> OS: Centos 6x
> tested system: 1g9v from Selfdocking dataset found at
> http://www.ysbl.york.ac.uk/rDock/test_data/Selfdock_Test.tar.gz
> tested commands:
> rbdock -i 1g9v_output.sd -r 1g9v.prm -p score.prm -n 1 -T 3 -o
> 1g9v_output_score > 1g9v_output_score.log
> rbdock -i 1g9v_output.sd -r 1g9v.prm -p score.prm -n 1 -T 3 >
> 1g9v_output_score_noOutput.log
> I can send the log files directly if requested.
>
>
> ------------------------------------------------------------------------------
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> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] problem with charge specification in SDF format

[Jose M. G. <jos...@un...>]

Hi all,

I have problem due to SDF format. I tried to dock this 3D molecule 
generated with RDKit:
MOL1
      RDKit          3D

   5  4  0  0  0  0  0  0  0  0999 V2000
     0.0381    0.0036    0.0029 C   0  0  0  0  0  0  0  0  0  0  0 0
     1.3529    0.1296    0.1027 O   0  0  0  0  0  0  0  0  0  0  0 0
    -0.5258   -0.1653    0.9360 H   0  0  0  0  0  0  0  0  0  0  0 0
    -0.5204    0.8550   -0.4220 H   0  0  0  0  0  0  0  0  0  0  0 0
    -0.3447   -0.8229   -0.6196 H   0  0  0  0  0  0  0  0  0  0  0 0
   1  2  1  0
   1  3  1  0
   1  4  1  0
   1  5  1  0
M  CHG  1   2  -1
M  END
$$$$

When running rbdock, I am getting this warning:
  **WARNING** RBT_MODEL_ERROR at ../src/lib/RbtMdlFileSource.cxx, line 405
O2 makes too few bonds

If I rewrite it with the charge specified in the atom block, I don't get 
the warning anymore:
MOL2
   Mrv0541 01051615193D

   5  4  0  0  0  0            999 V2000
     0.0381    0.0036    0.0029 C   0  0  0  0  0  0  0  0  0  0  0 0
     1.3529    0.1296    0.1027 O   0  5  0  0  0  0  0  0  0  0  0 0
    -0.5258   -0.1653    0.9360 H   0  0  0  0  0  0  0  0  0  0  0 0
    -0.5204    0.8550   -0.4220 H   0  0  0  0  0  0  0  0  0  0  0 0
    -0.3447   -0.8229   -0.6196 H   0  0  0  0  0  0  0  0  0  0  0 0
   1  2  1  0  0  0  0
   1  3  1  0  0  0  0
   1  4  1  0  0  0  0
   1  5  1  0  0  0  0
M  CHG  1   2  -1
M  END
$$$$

Does the problem come indeed from the flag in atom block?

If so, would it be possible to update the sdf parser so that it can 
detect charges directly from the M CHG statement?
I believe the docs indicate that this flag is actually deprecated (1). 
Did I miss something?

Thank you for your help!

Best regards,
Jose Manuel

(1) http://c4.cabrillo.edu/404/ctfile.pdf

[rDock-list-def] extract score from rescoring without writing a sd file

[Jose M. G. <jos...@un...>]

Hi,

I rescore poses using rbdock with the score.prm protocol as routine on a 
single molecule within a script.

I would like to avoid writing output files and just extract the SCORE 
and SCORE.INTER properties directly from the STDOUT.
However, when I remove the -o argument, I cannot access the scores at 
all and something like -o /dev/stdout returns an error since the 
programme still wants to write a file.

Is there a way to achieve this without modifying the source code (I 
don't know much about C++...!)?
If not, could you kindly tell me what I should change in the rbdock.cxx 
to make it work?

I also tried to use the -T argument but could not find the scores among 
the displayed info. Did I miss something?

Thank you for your help!

Cheers,
Jose Manuel

Supplementary information:
OS: Centos 6x
tested system: 1g9v from Selfdocking dataset found at 
http://www.ysbl.york.ac.uk/rDock/test_data/Selfdock_Test.tar.gz
tested commands:
rbdock -i 1g9v_output.sd -r 1g9v.prm -p score.prm -n 1 -T 3 -o 
1g9v_output_score > 1g9v_output_score.log
rbdock -i 1g9v_output.sd -r 1g9v.prm -p score.prm -n 1 -T 3 > 
1g9v_output_score_noOutput.log
I can send the log files directly if requested.

[rDock-list-def] extract rescoring score without rewriting a file

[Jose M. G. <jos...@un...>]

Hi,

I rescore poses using rbdock with the score.prm protocol as routine on a 
single molecule within a script.

I would like to avoid writing output files and just extract the SCORE 
and SCORE.INTER properties directly from the STDOUT.
However, when I remove the -o argument, I cannot access the scores at 
all and something like -o /dev/stdout returns an error since the 
programm still wants to write a file.

Is there a way to achieve this without modifying the source code (I 
don't know much about C++...!)?
If not, could you kindly tell me what I should change in the rbdock.cxx 
to make it work?

I also tried to use the -T argument but could not find the scores among 
the displayed info. Did I miss something?

Thank you for your help!

Cheers,
Jose Manuel


Supplementary information:
OS: Centos 6x
tested system: 1g9v from Selfdocking dataset found at 
http://www.ysbl.york.ac.uk/rDock/test_data/Selfdock_Test.tar.gz
attached files
1g9v_output_score.log: output from command:
rbdock -i 1g9v_output.sd -r 1g9v.prm -p score.prm -n 1 -T 3 -o 
1g9v_output_score > 1g9v_output_score.log
1g9v_output_score_noOutput.log: output from command:
rbdock -i 1g9v_output.sd -r 1g9v.prm -p score.prm -n 1 -T 3 > 
1g9v_output_score_noOutput.log

Re: [rDock-list-def] execution error

[Sergio R. C. <sru...@gm...>]

Hi Yocheved,

Have you defined the needed environment variables?
Double check that they are correct, please:

export RBT_ROOT=/path/to/rDock/installation/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RBT_ROOT/lib
export PATH=$PATH:$RBT_ROOT/bin

On easy thing you can try to check if your installation is correct is to go
to $RBT_ROOT/build and type "make test".
This will tell you if there is some error, otherwise it is installed
correctly.
Best,

Sergio

2015-09-10 11:20 GMT+02:00 Sergio Ruiz Carmona <sru...@gm...>:

> Hi Yocheved,
>
> Have you defined the neede environment variables??
>
>
> 2015-09-10 11:17 GMT+02:00 יוכבד <yb...@gm...>:
>
>> Hi
>>
>> I'm a new user and I'm having trouble with running an RDock simulation
>> and could really use your help.
>> I tried executing the rbcavity using a prm file and I got the following
>> message:
>>
>> RBT_FILE_READ_ERROR at ../src/lib/RbtBaseFileSource.cxx, line 233
>> Error opening
>> /private/gnss/rdock/rDock_2013.1_src/bin/data/RbtElements.dat
>>
>> the file RbtElements.dat exist and I'm able to open it so what am I doing
>> wrong?
>> Are there any input files (.prm .mol .sd) that I can use to see of the
>> implementation on my machine works at all?
>>
>> Thanks
>> Yocheved
>>
>>
>>
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>

Re: [rDock-list-def] execution error

[Sergio R. C. <sru...@gm...>]

Hi Yocheved,

Have you defined the neede environment variables??


2015-09-10 11:17 GMT+02:00 יוכבד <yb...@gm...>:

> Hi
>
> I'm a new user and I'm having trouble with running an RDock simulation and
> could really use your help.
> I tried executing the rbcavity using a prm file and I got the following
> message:
>
> RBT_FILE_READ_ERROR at ../src/lib/RbtBaseFileSource.cxx, line 233
> Error opening /private/gnss/rdock/rDock_2013.1_src/bin/data/RbtElements.dat
>
> the file RbtElements.dat exist and I'm able to open it so what am I doing
> wrong?
> Are there any input files (.prm .mol .sd) that I can use to see of the
> implementation on my machine works at all?
>
> Thanks
> Yocheved
>
>
>
> ------------------------------------------------------------------------------
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[rDock-list-def] execution error

[יוכבד <yb...@gm...>]

Hi

I'm a new user and I'm having trouble with running an RDock simulation and
could really use your help.
I tried executing the rbcavity using a prm file and I got the following
message:

RBT_FILE_READ_ERROR at ../src/lib/RbtBaseFileSource.cxx, line 233
Error opening /private/gnss/rdock/rDock_2013.1_src/bin/data/RbtElements.dat

the file RbtElements.dat exist and I'm able to open it so what am I doing
wrong?
Are there any input files (.prm .mol .sd) that I can use to see of the
implementation on my machine works at all?

Thanks
Yocheved

Re: [rDock-list-def] modify/use another force field for ligands

[Sergio R. C. <sru...@gm...>]

Dear Jose Manuel Gally,

As you said, Tripos 5.2 forcefield is used for the receptor.
Charmm27 and Insight parameters is only used when PSF/CRD files are
provided for the receptor. However, they are not used when the receptor is
in Mol2 format, as stated in rDock Documentation (Section 9):

MOL2 is now the preferred file format for rDock as it eliminates many of
> the atom typing issues inherent in
> preparing and loading PSF files. The use of PSF/CRD files is strongly
> discouraged. The recommendation
> is to prepare an all-atom MOL2 file with correct Tripos atom types
> assigned, and allow rDock to remove
> non-polar hydrogens on-the-fly.


The ligand forcefield is also Tripos 5.2 and can not be changed (without
modifying a lot of code).
For further information, more details about this can be found in
src/lib/RbtMdlFileSource.cxx and src/lib/RbtTriposAtomType.cxx.

Thank you!

Sergio Ruiz


2015-08-26 16:56 GMT+02:00 Jose Manuel Gally <
jos...@un...>:

> Dear rDock community,
>
> After docking molecules containing NH2 attached to aromatic ring (sp2
> nitrogen),  the two hydrogens are not in the same plane as the N-ring. I
> believe this issue came from the force field.
> I therefore analysed the force field used in rdock and noticed that
> several force fields are actually mentioned (in $RBT_HOME folder):
> - masses.rtf : Insight97and Charmm27
> - in folder sf, files Tripos52 (dihedral.prm, vdw.prm, vdw.prm.old)
>
> I think Tripos52 is applied to the receptor (correct me if I'm
> mistaken), but what for the ligand?
> How are used the parameters extracted from Charmm27 and Insight?
>
> Secondly, I would like to know if it's possible to modify/use another
> force field instead of the one implemented in rDock for ligands?
>
> Thank you for your help!
>
> Jose Manuel
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] modify/use another force field for ligands

[Jose M. G. <jos...@un...>]

Dear rDock community,

After docking molecules containing NH2 attached to aromatic ring (sp2 
nitrogen),  the two hydrogens are not in the same plane as the N-ring. I 
believe this issue came from the force field.
I therefore analysed the force field used in rdock and noticed that 
several force fields are actually mentioned (in $RBT_HOME folder):
- masses.rtf : Insight97and Charmm27
- in folder sf, files Tripos52 (dihedral.prm, vdw.prm, vdw.prm.old)

I think Tripos52 is applied to the receptor (correct me if I'm 
mistaken), but what for the ligand?
How are used the parameters extracted from Charmm27 and Insight?

Secondly, I would like to know if it's possible to modify/use another 
force field instead of the one implemented in rDock for ligands?

Thank you for your help!

Jose Manuel

Re: [rDock-list-def] Flexible docking

[Sergio R. C. <sru...@gm...>]

Dear Oscar,

rDock only takes into account full flexibility for the ligand.
However, terminal OH and NH3+ groups within RECEPTOR_FLEX distance of the
cavity defined will also be considered as flexible.
In section 8.1 of the documentation you have some more details about this
parameter:

RECEPTOR FLEX: Defines terminal OH and NH3+ groups within this distance of
docking volume as flexible. (default: 0, reasonable value: 3)

Best,

Sergio Ruiz


2015-05-19 12:03 GMT+02:00 Oscar Huertas <hu...@so...>:

> Hi all!
>
> I would like to know if is possible to run docking leaving some residues
> of the protein flexible or if is only possible with rigid protein.
>
> Thank you in advance for your answer.
>
> Oscar
>
>
>
>
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[rDock-list-def] Flexible docking

[Oscar H. <hu...@so...>]

Hi all!

I would like to know if is possible to run docking leaving some residues of
the protein flexible or if is only possible with rigid protein.

Thank you in advance for your answer.

Oscar 

 



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Re: [rDock-list-def] Which score should I use to get the best pose per ligand?

[Matthew L. <ml...@gm...>]

Hi Jose,

Exactly!  Personally, I use the SCORE term when I rank poses.  Now for
ranking compounds against each other, sometimes I use the SCORE term other
times I use the SCORE.INTER.  I typically pick whatever seems to correlate
with my data the most strongly (either my own, or things I find in
published articles).

Hope that helps!
Matthew


On Tue, May 12, 2015 at 7:53 AM, Jose Manuel Gally <
jos...@un...> wrote:

> Hi,
>
> I am scratching my head about when I should use rather SCORE or
> SCORE.INTER to get the best poses per ligand...
>
> In the ROC curve tutorial (1), the SCORE is used to sort the poses and
> get the best pose per ligand whereas SCORE.INTER is used to plot the ROC
> curve.
> In the HTVS tutorial (2), only SCORE.INTER is used to determine the best
> ligands at each step.
> In this thread (3) , Sergio explains how to get the top unique ligands
> with both scores.
>
> Is SCORE.INTER enough to determine the best poses per ligand? In what
> case is it better to use SCORE rather than SCORE.INTER?
>
>  From what I understood by reading the reference guide, SCORE.INTER is
> the weigthed sum of intermolecular interections and so represents the
> protein-ligand interactions, whereas SCORE represents the sum of all
> other scores (total score)...
>
> Thank you for your answer!
>
> Jose Manuel
>
> REFERENCES:
> (1) http://rdock.sourceforge.net/how-to-calculate-roc-curves/
> (2) http://rdock.sourceforge.net/multistep-protocol-for-htvs/
> (3) http://sourceforge.net/p/rdock/mailman/message/32567916/
>
>
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[rDock-list-def] Which score should I use to get the best pose per ligand?

[Jose M. G. <jos...@un...>]

Hi,

I am scratching my head about when I should use rather SCORE or 
SCORE.INTER to get the best poses per ligand...

In the ROC curve tutorial (1), the SCORE is used to sort the poses and 
get the best pose per ligand whereas SCORE.INTER is used to plot the ROC 
curve.
In the HTVS tutorial (2), only SCORE.INTER is used to determine the best 
ligands at each step.
In this thread (3) , Sergio explains how to get the top unique ligands 
with both scores.

Is SCORE.INTER enough to determine the best poses per ligand? In what 
case is it better to use SCORE rather than SCORE.INTER?

 From what I understood by reading the reference guide, SCORE.INTER is 
the weigthed sum of intermolecular interections and so represents the 
protein-ligand interactions, whereas SCORE represents the sum of all 
other scores (total score)...

Thank you for your answer!

Jose Manuel

REFERENCES:
(1) http://rdock.sourceforge.net/how-to-calculate-roc-curves/
(2) http://rdock.sourceforge.net/multistep-protocol-for-htvs/
(3) http://sourceforge.net/p/rdock/mailman/message/32567916/

Re: [rDock-list-def] Phosphoserine

[Daniel Á. G. <alg...@gm...>]

Hi Parker,

if you are using a mol2 file to define the receptor, rDock will read all
atomic information (including residue name and atom names) but will pay
special attention to the assigned Tripos atom types. As long as they are
correct for your modified residue atoms, it should work just fine with any
residue name. If your modified residue is charged (as I guess is the case),
things get a little more tricky:

In the full documentation section *9.1 Atomic properties* through
section *9.3 Parsing
a MOL2 file * (
http://rdock.sourceforge.net/wp-content/uploads/2014/06/rDock_User_Guide.pdf
) you will find that rDock does not read/use partial charges. So, no need
to worry about partial charges parameterization at all!  Instead, rDock
calculates formal charges for non-neutral residues (e.g. ASP residue will
have a total -1 charge divided into -0.5 assigned to each OD oxygen). And
here it comes the trick: When your modified residue bears any formal
charge, you will need to modify the lookup table to let rDock know! If you
don't do that, the residue will be neutral.

Find in section *9.5 Assigning distributed formal charges to the receptor * the
documentation about this issue. The solution is simple: you just need to
modify $RBT_ROOT/data/sf/RbtIonicAtoms.prm file to tell rDock that your
residuename XXX has a formal charge and how it is distributed among the
atoms. There is no information about the file format in the documentation,
but you will see it is pretty easy to understand and modify.

Summing up, if you have a neutral modified residue, making sure the
assigned tripos types in the input mol2 file are correct will do it. If the
residue is charged, modify the RbtIonicAtoms.prm lookup table to let rDock
know about the formal charge distribution within the residue atoms.

If you have any problem with the lookup table file format, write back ;)

Cheers!

Daniel



2015-02-21 17:27 GMT+01:00 Parker de Waal <Par...@va...>:

> Hi all,
>
> Does anyone m know how rDock handles modified residues?
>
> I'm working with a protein that is phosphorylated in the ligand binding
> pocket, however I can't find any documentation in the manual regarding
> residues such as this.
>
> Also, does rDock read charges from the mol2 receptor files? If this is the
> case I could apply charges from AMBER parameterization.
>
> Best,
> Parker
>
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-- 
Daniel Álvarez | PhD Student
dan...@ub...  | www.ub.edu/cbdd
Computational Biology and Drug Discovery Group
Faculty of Pharmacy | University of Barcelona

[rDock-list-def] Phosphoserine

[Parker de W. <Par...@va...>]

Hi all,

Does anyone m know how rDock handles modified residues?

I'm working with a protein that is phosphorylated in the ligand binding pocket, however I can't find any documentation in the manual regarding residues such as this.

Also, does rDock read charges from the mol2 receptor files? If this is the case I could apply charges from AMBER parameterization.

Best,
Parker

Re: [rDock-list-def] Pharmacophore

[Parker de W. <Par...@va...>]

Thank you Sergio,

My first test run went beautifully.

Regards,
Parker

On Feb 17, 2015 7:42 AM, Sergio Ruiz Carmona <sru...@gm...> wrote:
Dear Parker,

I have created a short tutorial to clarify this.
Please visit it here and don't hesitate to ask any questions if they are not clear enough.

http://rdock.sourceforge.net/pharmacophoric-restraints/<http://scanmail.trustwave.com/?c=129&d=z7bj1DyQbCJxZujCwwS5_L_xPwr92qe6uCn5_QDOSg&u=http%3a%2f%2frdock%2esourceforge%2enet%2fpharmacophoric-restraints%2f>

Best,
Sergio

2015-02-16 21:09 GMT+01:00 Parker de Waal <Par...@va...<mailto:Par...@va...>>:
Hi All,

After reading through the manual I’m having trouble understanding the format of the pharmacophore restraints file.

Does anyone have experience performing pharmacophore docking and have any insights in how to generate these input files?

Best,
Parker

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Re: [rDock-list-def] Pharmacophore

[Sergio R. C. <sru...@gm...>]

Dear Parker,

I have created a short tutorial to clarify this.
Please visit it here and don't hesitate to ask any questions if they are
not clear enough.

http://rdock.sourceforge.net/pharmacophoric-restraints/

Best,
Sergio

2015-02-16 21:09 GMT+01:00 Parker de Waal <Par...@va...>:

> Hi All,
>
> After reading through the manual I’m having trouble understanding the
> format of the pharmacophore restraints file.
>
> Does anyone have experience performing pharmacophore docking and have any
> insights in how to generate these input files?
>
> Best,
> Parker
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
>
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> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] Pharmacophore

[Parker de W. <Par...@va...>]

Hi All,

After reading through the manual I’m having trouble understanding the format of the pharmacophore restraints file.

Does anyone have experience performing pharmacophore docking and have any insights in how to generate these input files?

Best,
Parker

[rDock-list-def] Numerous warnings about undefined Tripos types for protein atoms

[Hassan G. <hg...@us...>]

Hi,

I'm using rDock version '2013.1' which I just downloaded and built from
source on Ubuntu 14.

When I run both rbcavity and rbdock I get numerous warnings of the
following sort:

RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:-_0.3716:NH1
RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:-_0.3716:NH2
RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:-_0.2463:OD1
RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:-_0.2463:OD2

I believe my receptor mol2 file has Tripos atom types in it. Here are a few
lines from the receptor mol2 file:


   2235  CB         1.4470  -16.9190   28.2910 C.3   177  ASP177      0.0760
   2236  CG         1.9440  -18.2290   28.8890 C.2   177  ASP177      0.3582
   2237  OD1        2.4870  -19.0550   28.1260 O.co2 177  ASP177     -0.2463
   2238  OD2        1.7740  -18.4410   30.1130 O.co2 177  ASP177     -0.2463
   2239  H01        0.9500  -17.1340   27.3450 H     177  ASP177      0.0402

I prepared this receptor file by using OpenBabel to convert the PDB to
mol2. The Tripos atom types are in the column immediately after the
coordinates. Is this not the correct place for the Tripos atom types to be
listed?

Thank you for your help. And as always, thank for your maintenance of a
great open source docking program.

Sincerely,
Hassan Ghani, MD